Slovenia's Tina Maze, the runaway World Cup leader, kept her momentum to snatch her first gold medal of the competition but her feat was obscured by her rival's crash and the decision to let the race go ahead late in the day when the light was fading.
Vonn, crowned world champion in the discipline in Val d'Isere four years ago, tumbled down the Streciher piste, breaking her shin and tearing ligaments in her right knee in a race taking place nearly four hours behind schedule.
After she had been flown to hospital, the American team said she would miss the rest of the season because of the injuries.
Fog had forced the organisers to delay the race 13 times and the start of the favourites was further postponed by the crash of a race steward after eight skiers had gone down.
Snow conditions and visibility had seriously worsened by the time the American four-times World Cup winner set off, only to suffer the most serious crash in her career.
"Vonn suffered a torn ACL and MCL in her right knee and a lateral tibial plateau fracture," the US team said in a statement.
The crash brought to an end an already troubled season for Vonn, who took a three-week break from racing over New Year to sort out personal and health problems.
Her team said she was expected to return to World Cup racing next season and to compete at next year's Winter Olympics in Sochi.
After her crash, pre-race favourites Maria Hoefl-Riesch of Germany and Austrian Anna Fenninger also failed to complete the course.
In spite of the controversy, the podium was a prestigious one, with Maze winning in one minute 35.39 seconds ahead of two event specialists and former medallists.
Lara Gut, who won two silver medals in Val d'Isere in 2009, was second, 0.38 behind, a great reward for the talented Swiss after she spent the whole of 2010 off through injury.
Vonn's compatriot Julia Mancuso was third, 0.52 adrift, for her eighth medal at either the worlds or the Olympics.
"I'm really sorry for Lindsey who took a too direct line. I regret her dreadful crash," said Maze, who watched in horror as her rival fell.
"I think my performance was solid, I attacked well, but it wasn't easy to manage the wait before the race. I tried to stay focused and determined," she added.
Scheduled for 1000 GMT, the race finally went ahead at 1330 GMT and ended up being the latest super-G in history. Skiers had been on the slope at 0730 to check the course.
As dusk fell on the Planai massif, the race was stopped after 37 skiers, preventing 22 later starters from racing.
Not long before the race was halted, 20-year-old Italian Sofia Goggia, who has never scored a World Cup point, seized her chance to finish fourth, missing the podium by 0.05 seconds, with bib number 33.
While Vonn was taken by helicopter to hospital in Salzburg, Maze was left to enjoy the second world title of her career after the giant slalom two years ago in Garmisch-Partenkirchen.
"First day, first gold, I'm excited. I stayed focused the whole day. I knew that today there would be a race," said the Slovenian, who will take part in all five disciplines in the coming fortnight and can hope for more medals.
The experienced Mancuso, silver medallist in the speciality in Garmisch, said it had been a tough day.
"It was by far the most difficult race in my career. You had to use your instinct but a first medal on the first day is a super result," she said.
The men's super-G is scheduled for Wednesday.
- Sports & Recreation